In roryk/bcbioRnaseq: RNA-Seq Utilities

Methods

RNA-seq counts were generated by bcbio and bcbioRNASeq using salmon [@salmon]. Counts were imported into R using tximport [@tximport] and DESeq2 [@DESeq2]. Gene annotations were obtained from Ensembl. Plots were generated by ggplot2 [@ggplot2]. Heatmaps were generated by pheatmap [@pheatmap].

R session information {.tabset}

markdownHeader("YAML params", level = 2)
print(params)

markdownHeader("`session_info()`", level = 2)
sessioninfo::session_info()

markdownHeader("`sessionInfo()`", level = 2)
utils::sessionInfo()

markdownHeader("`_setup.R`", level = 2)
readr::read_lines("_setup.R") %>% writeLines()